calculateLOH {beadarraySNP} | R Documentation

## Determine LOH in experiment

### Description

Using pairings of normal and tumor samples the LOH pattern is determined

### Usage

    calculateLOH(object, grouping, NorTum = "NorTum", ...)
    calculateLair(object, grouping = NULL, NorTum = "NorTum", min.intensity = NULL,
        use.homozygous.avg = FALSE)

### Arguments

`object` | SnpSetIllumina object
`grouping` | Factor to show which samples belong together (are of the same individual)
`NorTum` | character vector or factor. Elements containing "N" are considered to be the normal sample
`min.intensity` | numeric
`use.homozygous.avg` | logical
`...` | extra arguments for `link{heterozygousSNPs}`

### Details

The heterozygous SNPs of the normal sample are inspected for changes. SNPs where the genotype of the test sample are homozygous are set to `TRUE`

### Value

For calculateLOH a SnpSetIllumina object with `loh` and `nor.gt` matrices in assayData. `loh` is a logical matrix, and `nor.gt` is a character matrix containing the genotypes of the corresponding normal sample For calculateLair a SnpSetIllumina object with `lair` matrix in assayData. lair is the lesser allele intensity ratio. If a corresponding normal sample is found, it is taken as reference. Else the genotypes of normal samples are taken as a reference

### Author(s)

Jan Oosting

### See Also

`SnpSetIllumina-class`

[Package beadarraySNP version 1.60.0 Index]